Microsatellite analysis of Rosa damascena Mill. accessions reveals genetic similarity between genotypes used for rose oil production and old Damask rose varieties

Damask roses are grown in several European and Asiatic countries for rose oil production. Twenty-six oil-bearing Rosa damascena Mill. accessions and 13 garden Damask roses were assayed by molecular markers. Microsatellite genotyping demonstrated that R. damascena Mill. accessions from Bulgaria, Iran, and India and old European Damask rose varieties possess identical microsatellite profiles, suggesting a common origin. At the same time, the data indicated that modern industrial oil rose cultivation is based on a very narrow genepool and that oil rose collections contain many genetically identical accessions. The study of long-term vegetative propagation of the Damask roses also reveals high somatic stability for the microsatellite loci analyzed.     

Could taxonomic misnaming threaten the ex situ conservation and the usage of plant genetic resources?

Ex situ conservation of plant germplasm, especially seed banking, is a favourable and widely used method for the conservation of plant genetic resources (PGR). The long-term conservation of these resources is fundamental for food security and plant breeding in order to stem the losses in agrobiodiversity and to meet the global challenges that agriculture is facing. The conservation and accessibility of PGR relies on their correct taxonomic labelling and on the building of a searchable database that links ex situ collections together. In the current study, we analysed the impact of taxonomic misnaming in the two major PGR databases (Genesys PGR, EURISCO), listing accessions conserved worldwide. The aim was to understand if taxonomic misnaming issues prevent PGR conservation. We chose as a case-study seed collections of accessions of the genus Citrullus (watermelon genepool), the taxonomy and nomenclature of which have been largely revised in recent times. We observed that taxonomic misnaming greatly limits PGR conservation with only 3% of the accessions listed in the databases correctly named; moreover, 28% were affected by taxonomic errors that prevent the establishment of the accessions’ taxonomic identity, with consequences on their conservation and exploitation. The existence of the problem was also confirmed by the experimental propagation of three misnamed accessions. We suggest herein a series of actions that, put in place, could solve the extant misnaming issues in the databases and prevent their reoccurrence, allowing the correct conservation and the usability by the stakeholders of all the accessions.     

Genetic diversity,seed size associations and population structure of a core collection of common beans (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.)

Cultivated common bean germplasm is especially diverse due to the parallel domestication of two genepools in the Mesoamerican and Andean centers of diversity and introgression between these gene pools. Classification into morphological races has helped to provide a framework for utilization of this cultivated germplasm. Meanwhile, core collections along with molecular markers are useful tools for organizing and analyzing representative sets of these genotypes. In this study, we evaluated 604 accessions from the CIAT core germplasm collection representing wide genetic variability from both primary and secondary centers of diversity with a newly developed, fluorescent microsatellite marker set of 36 genomic and gene-based SSRs to determine molecular diversity and with seed protein analysis to determine phaseolin alleles. The entire collection could be divided into two genepools and five predominant races with the division between the Mesoamerica race and the Durango–Jalisco group showing strong support within the Mesoamerican genepool and the Nueva Granada and Peru races showing less diversity overall and some between-group admixture within the Andean genepool. The Chile race could not be distinguished within the Andean genepool but there was support for the Guatemala race within the Mesoamerican genepool and this race was unique in its high level of diversity and distance from other Mesoamerican races. Based on this population structure, significant associations were found between SSR loci and seed size characteristics, some on the same linkage group as the phaseolin locus, which previously had been associated with seed size, or in other regions of the genome. In conclusion, this study has shown that common bean has very significant population structure that can help guide the construction of genetic crosses that maximize diversity as well as serving as a basis for additional association studies.     

New gene-derived simple sequence repeat markers for common bean (Phaseolus vulgaris L.)

Common bean is an important and diverse crop legume with several wild relatives that are all part of the Phaseoleae tribe of tropical crop legumes. Sequence databases have been a good source of sequences to mine for simple sequence repeats (SSRs). The objective of this research was to evaluate 14 sequence collections from common bean for SSRs and to evaluate the diversity of the polymorphic microsatellites derived from these collections. SSRs were found in 10 of the GenBank sequence collections with an average of 11.3% of sequences containing microsatellite motifs. The most common motifs were based on tri- and dinucleotides. In a marker development programme, primers were designed for 125 microsatellites which were tested on a panel of 18 common bean genotypes. The markers were named as part of the bean microsatellite-database (BMd) series, and the average polymorphism information content was 0.404 for polymorphic markers and predicted well the genepool structure of common beans and the status of the wild and cultivated accessions that were included in the study. Therefore, the BMd series of microsatellites is useful for multiple studies of genetic relatedness and as anchor markers in future mapping of wide crosses in the species.     

AFLP diversity in the common vetch ( Vicia sativa L.) on the world scale

The Vavilov Institute of Plant Industry (VIR) keeps a living seed collection of about 700 accessions of landraces and local cultivars of common vetch ( Vicia sativa L.) that have been collected over a period of more than 50 years throughout the former USSR. Much of the material is available nowhere else. The collection of this economically important fodder crop is well adapted to the various growing regions of Russia and serves as a basis for the all domestic vetch breeding programs. Using AFLP as a DNA fingerprinting method we investigated 673 accessions from the VIR and compared their genetic variability with that of the worldwide vetch collection of the Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), 450 accessions. The analysis is a first assessment of the intra-specific diversity of V. sativa stored ex situ on a scale of more than 1,000 accessions. Six primer combinations, which gave clear polymorphic amplification products with 96 test samples, were chosen from 111 primer combinations tested. The selected AFLP primers used to analyse the V. sativa intra-specific diversity resulted in 70 unequivocally recognizable polymorphic fragments. We found that all of the AFLP fragments generated can be detected with varying frequency throughout the entire distribution area of V. sativa. The difference in frequency of some AFLP fragments between the regions may amount to 90%. The arrangement of most of the accessions in all dendrograms reflects their geographical origin, with a differentiation between Russia, Western Europe, Turkey and Bulgaria, and the Mediterranean. The "Russian" genepool stored at the IPK is a limited and biased sample of the available diversity when compared to the material stored at the VIR. Approximately 10-15% of the accessions in each geographical group showed AFLP patterns that clustered with members of other groups. This appreciable overlap raises several questions: (1) to which degree is an AFLP pattern representative of the overall genetic similarity of the samples; (2) to which degree are samples collected at a site adaptively limited to that site? Since our data identify accessions with very similar AFLP patterns from very diverse geographic origins, a comparison of the agronomic performance of these accessions (possibly in the two regions) will provide important information for the utilization of ex situ germplasm collections.     

Methods of developing a core collection of annual Medicago species

A core collection is a subset of a large germplasm collection that contains accessions chosen to represent the genetic variability of the germplasm collection. The purpose of the core collection is to improve management and use of a germplasm collection. Core collections are usually assembled by grouping accessions and selecting from within these groups. The objective of this study was to compare 11 methods of assembling a core collection of the U.S. National collection of annual Medicago species. These methods differed in their use of passport and evaluation data as well as their selection strategy. Another objective was to compare core collections with sample sizes of 5%, 10% and 17% of the germplasm collection. Core collections assembled with evaluation data and cluster analysis better represented the germplasm collection than core collections assembled based solely on passport data and random selection of accessions, The Relative Diversity and the logarithm methods generated better core collections than the proportional method. The 5% and 10% sample size core collection were judged insufficient to represent the germplasm collection.     

中国普通菜豆形态性状分析及分类

对129份中国普通菜豆地方品种的形态性状进行分析,结果表明,8个性状共检测到35个变异类型,平均变异类型为4.375个,平均多态信息含量为0.5638。中国普通菜豆包括安第斯和中美两个基因库种质,中美洲基因库资源在参试资源中比重较大,但安第斯基因库资源遗传多样性水平高于中美基因库材料。由中美基因库向安第斯基因库渗透的天然杂交种质可为普通菜豆高产、优质、抗逆育种提供有价值的桥梁品种。     

Unlocking variability: inherent variation and developmental traits of garlic plants originated from sexual reproduction

Recent collections of fertile garlic (Allium sativum) accessions from Central Asia allow a detailed study of seedling developments and the evaluation of inherent variations. We hereby provide a comprehensive account of the ontogenesis of a population of garlic seedlings and their vegetative and reproductive traits. A nucleotide binding site profiling marker technology was applied to provide conclusive evidence for the cross-pollination nature of garlic, and to compare the levels of polymorphism between progeny derived from a single mother clone fertilized by several pollinators. The seedlings’ population demonstrates a large variation in vegetative and reproductive characters, including bulbing ability, bulb color and size, clove number, and response to environmental conditions, similar to that of the genepool of vegetatively propagated garlic clones. In addition, a large variation in flowering and seed production ability was recorded. The understanding of garlic physiology, the availability of the large variability unleashed by sexual reproduction, and the possible utilization of sexual hybridization opens the way for genetic studies and breeding work. Haim D. Rabinowitch and Rina Kamenetsky contributed equally to this paper.     

A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley genome.

Direct estimates of sequence diversity provides an abundant source of DNA polymorphisms based on single nucleotide polymorphisms (SNPs). The frequency and distribution of nucleotide diversity within 23 genes associated with grain germination in barley were determined in a sample of accessions representing European cultivars, landraces, and wild barley accessions from throughout the fertile crescent. The overall nucleotide diversity ranged from 0.0021 to 0.0189 with a single nucleotide change being detected every 78 bp and insertion-deletion events being observed every 680 bp. Within the cultivated (H. vulgare) genepool, a small number of haplotypes were detected, the total number of haplotypes observed in H. spontaneum was almost double that detected in H. vulgare (46 and 26, respectively). Distinct haplotypes were observed in the H. spontaneum and landrace genepools, which are highly divergent from H. vulgare. A comparison of SNP-based haplotype data with EST-derived SSRs and genomic SSRs revealed a similar trend of decreasing variability in the cultivated genepool. However, the number of unique alleles identified in the cultivated sample was much greater with genomic SSRs (18%) compared with only 2.1% for SNPs and 3.8% for EST-derived SSRs. The potential utility of SNPs and EST-derived SSRs for association mapping in barley is discussed.     

Haplotype variation at Badh2, the gene determining fragrance in rice

Fragrance is an important component of end-use quality in rice. A set of 516 fragrant rice accessions were genotyped and over 80% of them carried the badh2.7 allele. A subset of 144 mostly fragrant accessions, including nine of Oryza rufipogon, was then subjected to a detailed diversity and haplotype analysis. The level of linkage disequilibrium in the Badh2 region was higher among the fragrant accessions. Re-sequencing in the Badh2 region showed that badh2.7, badh2.2 and badh2.4–5 all arose in the japonica genepool, and spread later into the indica genepool as a result of deliberate crossing. However, loss-of-function alleles of Badh2 are also found in the indica genepools, and then transferred into japonica. Evidence for three new possible FNPs was obtained from the Badh2 sequence of 62 fragrant accessions. Based on these data, we have elaborated a model for the evolution of Badh2 and its participation in the rice domestication process.     

高粱种质资源的多样性和利用

全世界收集到的高粱种质资源168500份,其中国际热带半干旱地区作物研究所有36774份,占总数的21.8%,美国42221份,占25.1%,印度20812份,占12.4%,中国12836份,占7.6%,其他国家55857份,占33.1%。上述国际研究所和国家在对高粱种质资源进行收集、整理、登记的基础上,对其遗传的多样性和各种性状做了鉴定,从中筛选出许多具有优良农艺性状、品质性状、抗性性状的资源,满足了高粱遗传改良的需要,成为当代和未来人类有价值的资源。建立核心种质对种质资源的保存、维护和利用是一种经济、实用和有效的方法。     

Genetic Relatedness among Lansium domesticum Accessions Using RAPD Markers

Genetic relatedness among 85 Lansium domesticum Corr. accessionsfrom Peninsular Malaysia were investigated using random amplifiedpolymorphic DNA (RAPD) markers. Ten primers were used for amplificationand yielded a total of 113 bands, of which 107 were polymorphic.Homology tests showed that the RAPD bands used in the studysatisfy assumptions of homology and non-allelic behaviour. Adendrogram showing genetic similarities among accessions wasconstructed based on the 107 polymorphic bands using UPGMA clusteranalysis. Jaccard similarity coefficients ranged from 0.25 to1.00 among accessions indicating a diverse genepool in the speciesindicative of different species parentage. The dendrogram separatedthe 85 accessions into three main clusters, one comprising 56accessions which possess thin-skinned fruit (mostly Dokong andLangsat), while the second has 28 accessions (mostly Duku-langsat,Duku Terengganu and Duku Johor) with thick fruit skin and thethird comprising only one accession, namely Duku hutan. Thus,RAPD analysis was a useful tool for determining the geneticrelatedness among accessions and identifying different typesof L. domesticum. Copyright 2000 Annals of Botany Company Lansium domesticum, genetic relatedness, RAPD markers, cluster analysis     

Genepool Variation in Genus Glycine Subgenus Soja Revealed by Polymorphic Nuclear and Chloroplast Microsatellites

A combination of nuclear and chloroplast simple sequence repeats (SSRs) have been used to investigate the levels and pattern of variability detected in Glycine max and G. soja genotypes. Based on the analysis of 700 soybean genotypes with 115 restriction fragment length polymorphism (RFLP) probes, 12 accessions were identified that represent 92% of the allelic variability detected in this genepool. These 12 core genotypes together with a sample of G. max and G. soja accessions were evaluated with 11 nuclear SSRs that detected 129 alleles. Compared with the other G. max and G. soja genotypes sampled, the core genotypes represent 40% of the allelic variability detected with SSRs. Despite the multi-allelic nature of soybean SSRs, dendrograms representing phenetic relationships between accessions clustered according to their subspecies origin. In addition to biparentally inherited nuclear SSRs, two uniparentally (maternally) transmitted chloroplast SSRs were also studied. A total of seven haplotypes were identified, and diversity indices of 0.405 +/- 0.088 and 0.159 +/- 0.071 were obtained for the two chloroplast SSRs. The availability of polymorphic SSR loci in the chloroplast genome provides new opportunities to investigate cytonuclear interactions in plants.     

西瓜种质资源抗旱性苗期筛选与评价

采用苗期持续干旱法,对1066份西瓜种质资源开展大规模抗旱性筛选评价。结果表明,不同基因型种质资源抗旱性差异明显。采用快速聚类方法将供试材料分为抗旱、耐旱、敏感和抗性分离等4种类型,共获得25份强抗旱性西瓜材料,多为来源于非洲的野生西瓜种质资源,适用于西瓜嫁接砧木的选育;获得30份中等抗旱性材料,多为栽培种西瓜种质资源,具有农艺性状优良、抗病性强等优点,可直接用于抗旱节水西瓜新品种选育。     

Assessment of genetic variation within Indian mustard (Brassica juncea) germplasm using random amplified polymorphic DNA markers

Genetic diversity among 45 Indian mustard (Brassica Juncea L.) genotypes comprising 37 germplasm collections, five advance breeding lines and three improved cultivars was investigated at the DNA level using the random amplified polymorphic DNA (RAPD) technique. Fifteen primers used generated a total of 92 RAPD fragments, of which 81 (88%) were polymorphic. Of these, 13 were unique to accession 'Pak85559'. Each primer produced four to nine amplified products with an average of 6.13 bands per primer. Based on pairwise comparisons of RAPD amplification products, Nei and Li's similarity coefficients were calculated to evaluate the relationships among the accessions. Pairwise similarity indices were higher among the oilseed accessions and cultivars showing narrow ranges of 0.77-0.99. An unweighted pair-group method with arithmetic averages cluster analysis based on these genetic similarities placed most of the collections and oilseed cultivars close to each other, showing a low level of polymorphism between the accessions used. However, the clusters formed by oilseed collections and cultivars were comparatively distinct from that of advanced breeding lines. Genetically, all of the accessions were classified into a few major groups and a number of individual accessions. Advanced breeding lines were relatively divergent from the rest of the accessions and formed independent clusters. Clustering of the accessions did not show any pattern of association between the RAPD markers and the collection sites. A low level of genetic variability of oilseed mustard was attributed to the selection for similar traits and horticultural uses. Perhaps close parentage of these accessions further contributed towards their little diversity. The study demonstrated that RAPD is a simple and fast technique to compare the genetic relationship and pattern of variation among the gene pool of this crop.     

Preservation of plant genetic resources in the biotechnology era

Thousands of years ago humans began domesticating crops as a food source. Among the wild germplasm available, they selected those that were best adapted for cultivation and utilization. Although wild ancestors have continued to persist in regions where domestication took place, there is a permanent risk of loss of the genetic variability of cultivated plants and their wild relatives in response to changing environmental conditions and cultural practices. Recognizing this danger, plant ex situ genebank collections were created since the beginning of the last century. World-wide, more than 6 million accessions have been accumulated including the German ex situ genebank in Gatersleben, one of the four largest global collections, housing 150,000 accessions belonging to 890 genera and 3032 species. This review summarizes the ex situ plant genetic resources conservation behavior with a special emphasis on German activities. Strategies for maintenance and management of germplasm collections are reviewed, considering modern biotechnologies (in vitro and cryo preservation). General aspects on genetic diversity and integrity are discussed.     

DNA fingerprinting and new tools for fine-scale discrimination of Arabidopsis thaliana accessions

One of the main strengths of Arabidopsis thaliana as a model species is the impressive number of public resources available to the scientific community. Exploring species genetic diversity--and therefore adaptation--relies on collections of individuals from natural populations taken from diverse environments. Nevertheless, due to a few mislabeling events or genotype mixtures, some variants available in stock centers have been misidentified, causing inconsistencies and limiting the potential of genetic analyses. To improve the identification of natural accessions, we genotyped 1311 seed stocks from our Versailles Arabidopsis Stock Center and from other collections to determine their molecular profiles at 341 single nucleotide polymorphism markers. These profiles were used to compare genotypes at both the intra- and inter-accession levels. We confirmed previously described inconsistencies and revealed new ones, and suggest likely identities for accessions whose lineage had been lost. We also developed two new tools: a minimal fingerprint computation to quickly verify the identity of an accession, and an optimized marker set to assist in the identification of unknown or mixed accessions. These tools are available on a dedicated web interface called ANATool (https://www.versailles.inra.fr/ijpb/crb/anatool) that provides a simple and efficient means to verify or determine the identity of A. thaliana accessions in any laboratory, without the need for any specific or expensive technology.     

High level of genetic diversity among spelt germplasm revealed by microsatellite markers.

The genetic diversity of spelt (Triticum aestivum (L.) Thell. subsp. spelta (L.) Thell.) cultivated presently is very narrow. Although the germplasm collections of spelt are extensive, the related genetic knowledge is often lacking and makes their use for genetic improvement difficult. The genetic diversity and structure of the spelt gene pool held in gene banks was determined using 19 simple sequence repeat (SSR) markers applied to 170 spelt accessions collected from 27 countries and 4 continents. The genetic distances (1 - proportion of shared alleles) were calculated and an unweighted pair-group method with arithmetic averaging (UPGMA)-based dendrogram was generated. The genetic diversity was high: 259 alleles were found and the mean interaccession genetic distance was 0.782 +/- 0.141. The dendrogram demonstrated the much higher genetic diversity of spelt held in germplasm collections than in the currently used genotypes. Accessions with the same geographical origin often tended to cluster together. Those from the Middle East were isolated first. All but one of the Spanish accessions were found in a unique subcluster. Most accessions from eastern Europe clustered together, while those from northwestern Europe were divided into two subclusters. The accessions from Africa and North America were not separated from the European ones. This analysis demonstrates the extent of genetic diversity of spelts held in germplasm collections and should help to widen the genetic basis of cultivated spelt in future breeding programs.     

Extracting samples of high diversity from thematic collections of large gene banks using a genetic-distance based approach

Background  

Breeding programs are usually reluctant to evaluate and use germplasm accessions other than the elite materials belonging to their advanced populations. The concept of core collections has been proposed to facilitate the access of potential users to samples of small sizes, representative of the genetic variability contained within the gene pool of a specific crop. The eventual large size of a core collection perpetuates the problem it was originally proposed to solve. The present study suggests that, in addition to the classic core collection concept, thematic core collections should be also developed for a specific crop, composed of a limited number of accessions, with a manageable size.